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Im, S.B., Gupta, S., Jain, M., Chande, A.T., Carleton, H.A., Jordan, I.K., and Rishishwar, L. Genome-enabled molecular subtyping and serotyping for Shiga toxin- producing Escherichia coli.
Front Sust Food Systems. In Press.
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Chande, A.T., Nagar, S.D., Rishishwar, L., Mariño-Ramírez, L., Medina-Rivas, M.A., Valderrama-Aguirre, A.E., Jordan, I.K., Gallo, J.E. 2021. The impact of ethnicity and genetic ancestry on disease prevalence and risk in Colombia.
Front Genet. 12: 690366.
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Nagar, S.D., Conley, A.B., Chande, A.T., Rishishwar, L., Sharma, S., Mariño-Ramírez, L., Aguinaga-Romero, G., González-Andrade, F., Jordan, I.K. 2021. Genetic ancestry and ethnic identity in Ecuador.
HGG Adv. 2: 100050.
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Etienne, K.A., Berkow, E.L., Gade, L., Nunnally, N., Lockhart, S.R., Beer, K., Jordan, I.K., Rishishwar, L., Litvintseva, A.P. 2021. Genomic Diversity of Azole Resistant Aspergillus fumigatus in the USA.
mBio. mBio 12: e0180321.
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Norris, E.T., Rishishwar, L., Jordan, I.K. 2021. Adaptive introgression for rapid human evolution in the Americas.
In: Muñoz, M.L., Crawford, M.H. (Eds.), Human Migration: Biocultural Perspectives. Oxford University Press.

Nagar, S.D., Nápoles, A.M., Jordan, I.K., Marinño-Ramírez, L. 2021. Socioeconomic deprivation and genetic ancestry interact to modify type 2 diabetes ethnic disparities in the United Kingdom.
EClinicalMedicine. 37:100960.
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Gallo, J.E., Torres, I., Gómez, O.M., Rishishwar, L., Vannberg, F., Jordan, I.K., McEwen, J.G., and Clay, O.K. 2021. New Histoplasma Diagnostic Assays Designed via Whole Genome Comparisons.
J. Fungi. 7: 544.
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Medina-Cordoba, L.K., Chande, A.T., Rishishwar, L., Mayer, L.W., Valderrama-Aguirre, L.C., Valderrama-Aguirre, A., Gaby, J.C., Kostka, J.E., and Jordan, I.K. 2021. Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields.
Sci Rep. 11: 9187.
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Band, V.I., Satola, S.W., Smith, R.D., Hufnagel, D.A., Bower, C., Conley, A.B., Rishishwar, L., Dale, S.E., Hardy, D.J., Vargas, R.L., Dumyati, G., Kainer, M.A., Phipps, E.C., Pierce, R., Wilson, L.E., Sorensen, M., Nilsson, E., Jordan, I.K., Burd, E.M., Farley, M.M., Jacob, J.T., Ernst, R.K., Weiss, D.S. 2021. Colistin heteroresistance is largely undetected among carbapenem-resistant Enterobacterales in the United States.
mBio. 12: e02881-20.
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Nagar, S.D., Conley, A.B, Jordan, I.K. 2021. Deconvolving human evolutionary history: using network-based approaches to better understand our past.
In: Wolkenhauer O. (Ed), Systems Medicine: Integrative, Qualitative and Computational Approaches (Vol. 3, pp. 105-110). Elsevier.
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Wozniak, J.E, Chande, A.T., Burd, E.M., Band, V.I., Satola, S.W., Farley, M.M., Jacob, J.T., Jordan, I.K., Weiss, D.S. 2020. Absence of mgrB Alleviates Negative Growth Effects of Colistin Resistance in Enterobacter cloacae.
Antiobiotics (Basel). 9: 825.
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Nagar, S.D., Conley, A.B., Jordan, I.K. 2020. Population structure and pharmacogenomic risk stratification in the United States.
BMC Biol. 18: 140.
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Chande, A.T., Rishishwar, L., Ban, D., Nagar, S.D., Conley, A.B., Rowell, J., Valderrama-Aguirre, A., Medina-Rivas, M.A., Jordan, I.K. 2020. The phenotypic and functional consequences of genetic divergence between admixed Latin American populations: Antioquia and Chocó, Colombia.
Genome Biol Evol. 12: 1516-1527.
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Espitia-Navarro, H.F., Chande, A.T., Nagar, S.D., Smith, H., Jordan, I.K. and Rishishwar, L. (2020) STing: accurate and ultrafast genomic profiling with exact sequence matches.
Nucleic Acids Res. 48: 7681-7689.
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Chande, A.T., Rishishwar, L., Conley, A.B., Valderrama-Aguirre, A., Medina-Rivas, M.A. and Jordan, I.K. 2020. Ancestry effects on type 2 diabetes genetic risk inference in Hispanic/Latino populations.
BMC Medical Genetics. 21: 132.
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Weitz, J.S., Harris, M., Chande, A.T., Gussler, J.W., Rishishwar, L. and Jordan, I.K. (2020) Online COVID-19 Dashboard Calculates How Risky Reopenings and Gatherings Can Be.
Sci Am.
[Scientific American]

Clayton, E.A., Rishishwar, L., Huang, T-C., Gulati, S., Ban, D., McDonald, J.F., and Jordan, I.K. 2020. An atlas of transposable element derived alternative splicing in cancer.
Philos Trans R Soc Lond B Biol Sci. 375: 20190342.
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Norris, E.T., Rishishwar, L., Chande, A.T., Conley, A.B., Ye, K., Valderrama-Aguirre, A., Jordan, I.K. 2020. Admixture-enabled selection for adaptive evolution in the Americas.
Genome Biol. 21: 29.
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Clayton, E.A., Khalid, S., Ban, D., Wang, L., Jordan, I.K., McDonald, J.F. 2020. Tumor suppressor genes and allele-specific expression: mechanisms and significance.
Oncotarget. 11: 462-479.
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Espitia-Navarro, H.F., Rishishwar, L., Mayer, L.W., Jordan, I.K. 2020. Bioinformatics: Rapid bacterial typing in the post-genomic era.
In: Budowle, B., Schutzer, S., and Morse, S. (Eds.), Microbial Forensics (3rd ed., pp. 267-282). Elsevier.
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Jordan, I.K., Rishishwar, L., Conley, A.B. 2019. Native American admixture recapitulates population-specific migration and settlement of the continental United States.
PLoS Genet. 15: e1008225.
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Crisan, C.V., Chande, A.T., Williams, K., Raghuram, V., Rishishwar, L., Steinbach, G., Watve, S.S., Yunker, P., Jordan, I.K. and Hammer, B.K. 2019. Analysis of Vibrio cholerae genomes identifies new Type VI Secretion System gene clusters.
Genome Biol. 20: 163.
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Kuruc, J.C., Durant-Archibold, A.A., Motta, J., Rao, K.S., Trachtenberg, B., Ramos, C., Wang, H., Gorenstein, D., Vannberg, F., Jordan, I.K. 2019. Development of anthracycline-induced dilated cardiomyopathy due to mutation on LMNA gene in a breast cancer patient: a case report.
BMC Cardiovasc Disord. 19: 169.
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Norris, E.T, Rishishwar, L., Wang, L., Conley, A.B., Chande, A.T., Dabrowski, A.M., Valderrama-Aguirre, A., Jordan, I.K. 2019. Assortative mating on ancestry-variant traits in admixed Latin American populations.
Front Genet. 10: 359.
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Wozniak, J.E., Band, V.I., Conley, A.B., Rishishwar, L., Burd, E.M., Satola, S.W., Hardy, D, Tsay, R., Farley, M.M., Jacob, J., Dumyati, G., Jordan, I.K., Weiss, D.S. 2019. A Nationwide Screen of carbapenem-resistant Klebsiella pneumoniae reveals an isolate with enhanced virulence and clinically undetected colistin-heteroresistance.
Antimicrob Agents Chemother. 63: e00107-19.
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Nagar, S.D., Moreno, A.M., Norris, E.T., Rishishwar, L., Conley, A.B., O'Neal, K.L., Vélez-Gómez, S., Montes-Rodríguez, C., Jaraba-Álvarez, W.V., Torres, I., Medina-Rivas, M.A., Valderrama-Aguirre, A.E., Jordan, I.K., Gallo, J.E. 2019. Population pharmacogenomics for precision public health in Colombia.
Front Genet. 10: 241.
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Bernardy, E.E., Petit, R., Moller, A., Blumenthal, J., McAdam, A., Priebe, G., Chande, A.T., Rishishwar, L., Jordan, I.K., Read, T., Goldberg, J. 2019. Whole Genome Sequence of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections.
Microbiol Resour Announc. 8: e01564-18.
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Norris, E.T., Wang, L., Conley, A.B., Rishishwar, L., Mariño-Ramírez, L., Valderrama-Aguirre, A., Jordan, I.K., 2018. Genetic ancestry, admixture and health determinants in Latin America.
BMC Genomics. 19: 861.
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Rishishwar, L., Wang, L., Wang, J., Yi, S.V., Lachance, J., Jordan, I.K., 2018. Evidence for positive selection on recent human transposable element insertions
Gene. 675: 69-79.
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Chande, A.T., Wang, L., Rishishwar, L., Conley, A.B., Norris, E.T., Valderrama-Aguirre, A., Jordan, I.K., 2018. GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.
Nucleic Acids Res. 46: W121–W126.
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Medina-Cordoba, L.K., Chande, A.T, Rishishwar, L., Mayer, L.W., Mariño-Ramírez, L., Valderrama-Aguirre, L., Valderrama-Aguirre, A., Kostka, J.E, Jordan, I.K., 2018. Genome sequences of 15 Klebsiella spp. isolates from sugarcane fields in Colombia’s Cauca Valley.
Genome Announc. 6: e00104-18.
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Wang, L., Jordan, I.K., 2018. Transposable element activity, genome regulation and human health.
Curr Opin Genet Dev. 49: 25–33.
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Gaby, J.C., Rishishwar, L., Valderrama-Aguirre, L., Green, S.J., Valderrama-Aguirre, A., Jordan, I.K., Kostka , J.E., 2018. Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline.
Appl Environ Microbiol. 84: e01512-17.
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Chande, A.T., Rowell, J., Rishishwar, L., Conley, A.B., Norris, E.T., Valderrama-Aguirre, A., Medina-Rivas, M., Jordan, I.K., 2017. Influence of genetic ancestry and socioeconomic status on type 2 diabetes in the diverse Colombian populations of Chocó and Antioquia.
Sci Rep. 7: 17127.
[PubMed] [PDF] [Supplement]

Rishishwar, L., Mariño-Ramírez, L., and Jordan, I.K., 2017. Benchmarking computational tools for polymorphic transposable element detection.
Brief Bioinform. 18: 908–918.
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Morris, L.P., Conley, A.B., Degtyareva, N., Jordan, I.K., Doetsch, P.W., 2017. Genome-wide map of Apn1 binding sites under oxidative stress in Saccharomyces cerevisiae.
Yeast. 34: 447–458.
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Conley, A.B., Rishishwar, L., Norris, E.T., Valderrama-Aguirre, A., Mariño-Ramírez, L., Medina-Rivas, M., Jordan, I.K., 2017. A comparative analysis of genetic ancestry and admixture in the Colombian populations of Chocó and Medellín.
G3: Genes, Genomes, Genetics. 7: 3435-3447.
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Gaur, M., Wang, L., Amaro-Ortiz, A., Dobke, M., Jordan, I.K., Lunyak, V.V., 2017. Acute genotoxic stress-induced senescence in human mesenchymal cells drives a unique composition of senescence messaging secretome (SMS).
Journal of Stem Cell Research & Therapy. 7: 396.
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Wang, L., Norris, E.T., Jordan, I.K., 2017. Human retrotransposon insertion polymorphisms are associated with health and disease via gene regulatory phenotypes.
Front Microbiol. 8: 1418.
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Sepúlveda-Torres, L.d.C., Rishishwar L., Rogers, M.L., Ríos-Olivares, E., Boukli, N., Jordan, I.K., Cubano, L.A., 2017. A decade of viral mutations and associated drug resistance in a population of HIV-1+ Puerto Ricans: 2002–2011
PLoS One. 12: e0177452.
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Lopez, M.F., Niu, P., Wang, L., Vogelsang, M., Gaur, M., Krastins, B., Zhao, Y., Smagul, A., Nussupbekova, A., Akanov, A.A., Jordan, I.K., and Lunyak, V.V., 2017. Opposing activities of oncogenic MIR17HG and tumor suppressive MIR100HG clusters and their gene targets regulate replicative senescence in human adult stem cells.
NPJ Aging Mech Dis. 3: 7.
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Wang, L., Rishishwar, L., Mariño-Ramírez, L. and Jordan I.K., 2017. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.
Nuc Acids Res. 45: 2318–2328.
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Rishishwar, L. and Jordan, I.K., 2017. Implications of human evolution and admixture for mitochondrial replacement therapy.
BMC Genomics. 18: 140.
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Rishishwar, L., Wang, L., Clayton, E.A., Mariño-Ramírez, L., McDonald, J.F. and Jordan I.K., 2017. Population and clinical genetics of human transposable elements in the (post) genomic era.
Mob Genet Elements. 7: 1-20.
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Gupta, A., Jordan, I.K., Rishishwar, L., 2017. stringMLST: a fast k-mer based tool for multi locus sequence typing.
Bioinformatics. 33: 119-121.
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Topaz, N., Mojib, N., Chande, A.T., Kubanek, J., Jordan, I.K., 2017. RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions.
Database. 2017: bax067.
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Clayton, E.A., Wang, L., Rishishwar, L., Wang, J., McDonald, J.F. and Jordan I.K., 2016. Patterns of transposable element expression and insertion in cancer.
Front Mol Biosci. 3: 76.
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Watve, S., Chande, A.T., Rishishwar, L., Bernardy, E.E., Mariño-Ramírez, L., Jordan, I.K., Hammer, B.K., 2016. Whole genome sequence of 26 environmental Vibrio cholerae isolates.
Genome Announc. 4: e01396-16
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Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G.J., Jordan, I.K., Murphy, T.F., Gilsdorf, J.R., Mayer, L.W., and Wang, X., 2016. Comparative genomic analysis of Haemophilus haemolyticus and non-typeable Haemophilus influenzae and a new testing scheme for their discrimination.
J Clin Micro. 54: 3010-3017.
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Orata, F.D., Xu, Y., Gladney, L.M., Rishishwar, L., Case, R.J., Boucher, Y., Jordan, I.K., Tarr, C.L., 2016. Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis.
Int J Syst Evol Microbiol. 66: 4148-4155.
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Rishishwar, L., Kraft, C.S., Jordan, I.K., 2016. Population genomics of reduced vancomycin susceptibility in Staphylococcus aureus.
mSphere. 1: e00094-16
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Jordan, I.K., 2016. The Columbian Exchange as a source of adaptive introgression in human populations.
Biol Direct. 11: 17
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Hemme, C.L., Green, S.J., Rishishwar, L., Prakash, O., Pettenato, A., Chakraborty, R., Deutchbauer, A.M., Van Nostrand, J.D., Wu, L., He, L., Jordan, I.K., Hazen, T.C., Arkin, A.P., Kostka, J.E. and Zhou, J., 2016. Lateral gene transfer in a heavy metal-contaminated groundwater microbial community.
mBio. 7: e02234-15
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Medina Rivas, M.A., Norris, E.T., Rishishwar, L., Conley, A.B., Medrano Trochez, C., Valderrama-Aguirre, A., Vannberg, F.O., Mariño-Ramírez, L., and Jordan, I.K., 2016. El Chocó Colombia: a hotspot of human biodiversity.
Rev. Biodivers. Neotrop. 6: 45-54
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Rishishwar, L., Tellez Villa, C.E. and Jordan, I.K., 2015. Transposable element polymorphisms recapitulate human evolution.
Mob. DNA. 6: 21
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Rishishwar, L., Conley, A.B., Vidakovic, B. and Jordan, I.K., 2015. A combined evidence Bayesian method for human ancestry inference applied to Afro-Colombians.
Gene. 574: 345-351
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Wang, X., Jordan, I.K., Mayer, L.W., 2015. A phylogenetic perspective on molecular epidemiology.
Molecular Medical Microbiology (Second Edition). 1: 517-536
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Niu, P., Smagul, A., Wang, L., Sadvakas, A., Sha, Y., Pérez, L.M., Nussupbekova, A., Amirbekov, A., Akanov, A.A., Gálvez, B.G., Jordan, I.K. and Lunyak, V., 2015. Transcriptional profiling of interleukin-2-primed human adipose derived mesenchymal stem cells revealed dramatic changes in stem cells response imposed by replicative senescence.
Oncotarget. 6: 17938-57.
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Wang, J., Vicente-García, C., Seruggia, D., Moltó, E., Fernandez-Miñán, A., Neto, A., Lee, E., Gómez-Skarmeta, J.L., Montoliu, L., Lunyak, V. and Jordan, I.K., 2015. MIR retotransposon sequences provide insulators to the human genome.
Proc. Natl. Acad. Sci. USA. 112: E4428-4437.
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Rishishwar, L., Conley, A.B., Wigington, C.H., Wang, L., Valderrama-Aguirre, A. and Jordan, I.K., 2015. Ancestry, admixture and fitness in Colombian genomes.
Sci Rep. 5: 12376
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Gladney, L.M., Katz, L., Knipe, K.M., Rowe, L., Conley, A.B., Rishishwar, L., Mariño-Ramírez, L., Jordan, I.K., and Tarr, C.L., 2014. Genome Sequences of Vibrio navarrensis, a Potential Human Pathogen.
Genome Announc. 2: e01188-14
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Castillo, A., Wang, L., Koriyama, C., Eizuru, Y., Jordan, I.K., and Akiba, S., 2014. A systems biology analysis of the changes in gene expression via silencing of HPV-18 E1 expression in HeLa cells.
Open Biol. 4: 130119
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Jjingo, D., Conley, A.B., Wang, J., Mariño-Ramírez, L., Lunyak, V.V., and Jordan, I.K., 2014. Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression.
Mob DNA. 5: 14
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Dunn, J., Qiu, H., Kim, S., Jjingo, D., Hoffman, R., Kim, C.W., Jang, I., Son, D.J., Kim, D., Pan, C., Fan, Y., Jordan, I.K., and Jo, H., 2014. Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis.
J Clin Invest. 124: 3187-3199
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Hu, B., Ying, X., Wang, J., Piriyapongsa, J., Jordan, I.K., Sheng, J., Yu, F., Zhao, P., Li, Y., Wang, H., Ng, W.L., Hu, S., Wang, X., Wang, C., Zheng, X., Li, W., Curran, W.J., and Wang, Y., 2014. Identification of a tumor suppressive human specific microRNA within the FHIT tumor suppressor gene.
Cancer Res. 74: 2283-94
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Rishishwar, L., Petit, R., Kraft, C.S., and Jordan, I.K., 2014. A genome sequence based discriminator for vancomycin-intermediate Staphylococcus aureus.
J Bacteriol. 196: 940-948
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Lopes, F.R., Jjingo, D., da Silva, C.R.M., Andrade, A.C., Marraccini, P., Teixeira, J.B., Carazzolle, M.F., Pereira, G.A.G., Pereira, L.P.F., Vanzela, A.L.L., Wang, L., Jordan, I.K., and Carareto, C.M.A., 2013. Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes.
PLoS ONE 8: e78931
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Jjingo, D., Wang, J., Conley, A.B., Lunyak, V.V., and Jordan, I.K, 2013. Compound cis-regulatory elements with both boundary and enhancer sequences in the human genome.
Bioinformatics 29: 3109-3112
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Zhoa, Y., Jordan, I.K. and Lunyak, V.V., 2013. Epigenetics components of aging in the central nervous system.
Neurotherapeutics 10: 647-663
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Green, S., Rishishwar, L., Prakash, O., Jordan, I.K. and Kostka, J., 2013. Insights into environmental microbial denitrification from integrated metagenomic, cultivation and genomic analyses.
In: Encyclopedia of Metagenomics, (Nelson, K. ed.) Springer, Berlin.

Sebastian, A., Rishishwar, L., Wang, J., Bernard, K.F., Conley, A.B., McCarty, N.A. and Jordan, I.K., 2013. Origin and evolution of the cystic fibrosis transmembrane regulator protein R domain.
Gene 523: 137-146
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Wang, J., Lunyak, V.V. and Jordan, I.K., 2013. BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
Bioinformatics 29: 492-493
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Lopez, M.F., Tollervey, J., Krastins, B., Garces, A., Sarracino, D., Prakash, A., Vogelsang, M., Geesman, G., Valderrama, A., Jordan, I.K. and Lunyak, V.V., 2012. Depletion of nuclear histone H2A variants is associated with chronic DNA damage signaling upon drug-evoked senescence of human somatic cells.
Aging 4: 823-842
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Conley, A.B. and Jordan, I.K., 2012. Cell type-specific termination of transcription by transposable element sequences.
Mob DNA. 3: 15
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Wang, J., Lunyak, V.V. and Jordan, I.K., 2012. Chromatin signature discovery via histone modification profile alignments.
Nucleic Acids Res. 40: 10642-10656
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Rishishwar, L., Katz, L.S., Sharma, N.V., Rowe, L., Frace, M., Dolan Thomas,J., Harcourt, B.H., Mayer, L.W. and Jordan, I.K., 2012. Genomic basis of a polyagglutinating isolate of Neisseria meningitidis.
J Bacteriol. 194: 5649-5656
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Rishishwar, L., Varghese, N., Tyagi, E., Harvey, S.C., Jordan, I.K. and McCarty, N.A., 2012. Relating the disease mutation spectrum to the evolution of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).
PLoS ONE 7: e42336
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Kostka, J.E., Green, S.J., Rishishwar, L., Prakash, O., Katz, L.S., Marino-Ramirez, L., Jordan, I.K., Watson, D.B., Brown, S.D., Palumbo, A.V. and Brooks, S.C., 2012. Genome sequences for six Rhodanobacter strains isolated from soils and the terrestrial subsurface with variable denitrification capabilities.
J. Bacteriol. 194: 4461
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Jjingo, D., Conley, A.B., Yi, S.V., Lunyak, V.V. and Jordan, I.K., 2012. On the presence and role of human gene-body DNA methylation.
Oncotarget 3: 462-474
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Lee, K.J., Conley, A.B., Lunyak, V.V. and Jordan, I.K., 2012. Do human transposable element small RNAs serve primarily as genome defenders or genome regulators?
Mob Genet Elements. 2: 1–7
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Blackwell, B., Lopez M.F., Wang, J., Krastins, B., Sarracino, D., Tollervey, J.R., Dobke, M.,Jordan, I.K. and Lunyak, V.V., 2012. Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly
Mob Genet Elements. 2: 1–10
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Conley, A.B. and Jordan, I.K., 2012. Epigenetic regulation of human cis-natural antisense transcripts.
Nucleic Acids Res. 40: 1438–1445
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Wang, J., Lunyak, V.V., and Jordan, I.K., 2012. Genome-wide prediction and analysis of human chromatin boundary elements.
Nucleic Acids Res. 40: 511-529
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Piriyapongsa, J., Jordan, I.K., Conley, A.B., Ronan, T. and N.R. Smalheiser, 2011. Transcription factor binding sites are highly enriched within microRNA precursor sequences.
Biol Direct. 6: 61
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Huda, A., Tyagi, E., Mariño-Ramírez, L., Bowen, N.J., Jjingo, D. and Jordan, I.K., 2011. Prediction of transposable element derived enhancers using chromatin modification profiles.
PLoS ONE 6: e27513
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Katz, L.S., Humphrey, J.C., Conley, A.B., Nelakuditi, V., Kislyuk, A.O., Agrawal, S., Jayaraman, P., Harcourt, B.H., Olsen- Rasmussen, M.A., Frace, M., Sharma, N.V., Mayer, L.W. and Jordan, I.K., 2011. Neisseria Base: a comparative genomics database for Neisseria meningitidis.
Database. 2011: bar035
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González Pérez, M., Murcia, M., Landsman, D., Jordan, I.K. and Mariño-Ramírez, L., 2011. The genome sequence of Mycobacterium colombiense CECT 3035 type strain.
J Bacteriol. 193: 5866–5867
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Jordan, I.K., Conley, A., Antonov, I., Arthur, R., Cook, E., Cooper, G., Jones, B., Knipe, K., Lee, K., Liu, X., Mitchell, G., Pande, P., Petit, R., Qin, S., Rajan, V., Sarda, S., Sebastian, A., Tang, S., Thapliyal, R., Varghese, N., Ye, T., Katz, L.S., Wang, X., Rowe, L., Frace, M. and Mayer, L., 2011. Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus.
J Bacteriol. 193: 5879–5880
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Wang, J., Geesman, G.J., Hostikka, S.L., Atallah, M., Blackwell, B., Lee, E., Cook, P.J., Pasaniuc, B., Shariat, G., Halperin, E., Dobke, M., Rosenfeld, M.G., Jordan, I.K. and Lunyak, V.V., 2011. Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal.
Cell Cycle 10: 3016-3030
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Katz, L.S., Sharma, N.V., Harcourt, B.H., Thomas, J.D., Wang, X., Mayer L.W. and Jordan, I.K., 2011. Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis.
J Bacteriol. 193: 3633-3641
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Jordan, K., 2011. Computational approaches for the transcriptomics, proteomics and epigenetic analysis in adult stem cells.
Cell Cycle. 10: 4187
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Momin, A.A., Park, H., Portz, B.J., Haynes, C.A., Shaner, R.L., Kelly, S.L., Jordan, I.K. and Merrill Jr., A.H., 2011. A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences.
J Lipid Res. 52: 1073-1083
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Jjingo, D., Huda, A., Gundapuneni, M., Mariño-Ramírez, L. and Jordan, I.K., 2011. Effect of the transposable element environment of human genes on gene length and expression.
Genome Biol. Evol. 3: 259-271
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Huda, A., Bowen, N.J., Conley, A.B. and Jordan, I.K., 2011. Epigenetic regulation of transposable element derived human gene promoters.
Gene 475: 39-48
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Wang, J., Huda, A., Lunyak, V.V. and Jordan, I.K., 2010. A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags.
Bioinformatics 26: 2501-2508
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Conley, A.B. and Jordan, I.K., 2010. Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.
Methods Mol. Biol. 674: 225-240
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Kislyuk, A.O., Katz, L.S., Agrawal, S., Hagen, M.S., Conley, A.B., Jayaraman, P., Nelakuditi V., Humphrey, J.C., Sammons, S.A., Govil, D., Mair, R.D., Tatti, K.M., Tondella, M.L., Harcourt, B.H., Mayer, L.W. and Jordan, I.K., 2010. A computational genomics pipeline for prokaryotic sequencing projects.
Bioinformatics 26: 1819-1826
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Huda, A., Mariño-Ramírez, L. and Jordan, I.K., 2010. Epigenetic histone modifications of human transposable elements: genome defense versus exaptation.
Mob DNA. 1: 2
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Wang, J., Bowen, N.J., Mariño-Ramírez, L. and Jordan, I.K., 2009. A c-Myc regulatory subnetwork from human transposable element sequences.
Mol Biosyst 5: 1831-1839
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Huda, A. and Jordan, I.K., 2009. Epigenetic regulation of mammalian genomes by transposable elements.
Ann NY Acad. Sci. 1178: 276-284
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Katz, L.S., Bolen, C.R., Harcourt B.H., Schmink S., Wang X., Kislyuk, A., Taylor, R.T., Mayer, L.W. and Jordan, I.K., 2009. Meningococcus Genome Informatics Platform: a system for analyzing multilocus sequence typing data.
Nucleic Acids Res 37: W606-W611
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Huda, A., Mariño-Ramírez, L., Landsman, D. and Jordan, I.K., 2009. Repetitive DNA elements, nucleosome binding and human gene expression.
Gene 436: 12-22
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Huda, A. and Jordan, I.K., 2009. Analysis of transposable element sequences using CENSOR and RepeatMasker.
Methods Mol. Biol. 537: 323-336
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Jordan, I.K., Kota, K.C., Cui, G., Thompson, C.H. and McCarty, N.A., 2008. Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters.
Proc. Natl. Acad. Sci. USA 105: 18865-18870
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Jordan, I.K., Katz, L.S., Denver, D.R. and J.T. Streelman, 2008. Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans.
BMC Syst Biol 2: 96
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Jordan, I.K. and Miller, W.M., 2008. Genome defense against transposable elements and the origins of regulatory RNA. In: Genome Dynamics and Stability, (Lankenau, D.H. and S. Scharz eds.) Springer, Berlin
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Jordan, I.K. and Koonin, E.V., 2008. Comparative human genomics. In: Handbook of Human Molecular Evolution, (Cooper, D.N. and H. Kehrer-Sawatzki eds.) John Wiley and Sons, London

Conley, A.B., Piriyapongsa, J. and Jordan, I.K., 2008. Retroviral promoters in the human genome.
Bioinformatics 24: 1563-1567
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Polavarapu, N., Mariño-Ramírez, L., Landsman, D., McDonald, J.F. and Jordan, I.K., 2008. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.
BMC Genomics 9: 226
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Antezana, M. and Jordan, I.K., 2008. Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes.
PLoS ONE 3: e2145
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Piriyapongsa, J. and Jordan, I.K., 2008. Dual coding of siRNAs and miRNAs by plant transposable elements.
RNA 14: 814-821
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Huda, A., Polavarapu, N., Jordan, I.K. and McDonald, J.F., 2008. Endogenous retroviruses of the chicken genome.
Biol Direct. 3: 9
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Conley, A.B., Miller, W.J. and Jordan, I.K., 2008. Human cis natural antisense transcripts initiated by transposable elements.
Trends Genet. 24: 53-56
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Piriyapongsa, J., Rutledge, M.T., Patel, S., Borodovsky, M. and Jordan, I.K., 2007. Evaluating the protein coding potential of exonized transposable element sequences.
Biol Direct. 2: 31
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Bowen, N.J. and Jordan, I.K., 2007. Exaptation of protein coding sequences from transposable elements.
Genome Dynamics 3: 131-146
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Jordan, I.K. and L. Mariño-Ramírez, 2007. Evolutionary genomics of gene expression. In: Structural approaches to sequence evolution: Molecules, networks, populations, (Bastolla, U., Porto, M., Roman, H.E. and M. Vendruscolo eds.), Springer, New York
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Piriyapongsa, J., Mariño-Ramírez, L. and Jordan, I.K., 2007. Origin and evolution of human microRNAs from transposable elements.
Genetics 176: 1323-1337
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Piriyapongsa, J. and Jordan, I.K., 2007. A family of human microRNA genes from miniature-inverted repeat transposable elements.
PLoS ONE 2: e203
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Mariño-Ramírez, L., Jordan, I.K. and Landsman, D., 2006. Multiple independent evolutionary solutions to core histone gene regulation.
Genome Biol. 7: R122
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Mariño-Ramírez, L., Bodenreider, O., Kantz, N. and Jordan, I.K., 2006. Co-evolutionary rates of functionally related yeast genes.
Evol Bioinform. Online 2: 295-300
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Tsaparas, P., Mariño-Ramírez, L., Bodenreider, O., Koonin, E.V. and Jordan, I.K., 2006. Global similarity and local divergence in human and mouse gene co-expression networks.
BMC Evol. Biol. 6: 70
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Jordan, I.K., Kondrashov, F.A., Adzhubei, I.A., Wolf, Y.I., Koonin, E.V., Kondrashov, A.S. and Sunyaev, S., 2006. Protein evolution: Causes of trends in amino-acid gain and loss (Reply).
Nature 442: E12
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Mariño-Ramírez, L. and Jordan, I.K., 2006. Transposable element derived DNaseI-hypersensitive sites in the human genome.
Biol Direct. 1:20
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Jordan, I.K., 2006. Evolutionary tinkering with transposable elements.
Proc. Natl. Acad. Sci. USA 96: 12621-12625
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Mariño-Ramírez, L., Lewis, K.C., Landsman, D. and Jordan, I.K., 2005. Transposable elements donate lineage-specific regulatory elements to host genomes.
Cytogenet. Genome Res. 110: 333-341
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Rogozin, I.B., Basu, M.K., Jordan, I.K., Pavlov, Y.I. and Koonin, E.V., 2005. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis.
Cell Cycle 4: 1281-1285
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Jordan, I.K., Mariño-Ramírez, L. and Koonin, E.V., 2005. Evolutionary significance of gene expression divergence.
Gene 345: 119-126
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Jordan, I.K., Kondrashov, F.A., Adzhubei, I.A., Wolf, Y.I., Koonin, E.V., Kondrashov, A.S. and Sunyaev, S., 2005. A universal trend of amino acid gain and loss in protein evolution.
Nature 433: 633-638
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Jordan, I.K., Mariño-Ramírez, L., Wolf, Y.I. and Koonin, E.V., 2004. Conservation and co-evolution in the scale-free human gene co-expression network.
Mol. Biol. Evol. 21: 2058-2070
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Jordan, I.K., Wolf, Y.I. and Koonin, E.V., 2004. Duplicated genes evolve slower than singletons despite the initial rate increase.
BMC Evol Biol. 4: 22
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Jordan, I.K. and Koonin, E.V., 2004. Horizontal transfer and prokaryotic genome evolution. Microbial Evolution: Gene Establishment, Survival and Exchange (Day, M. and B. Miller eds.), ASM Press, Washington, DC
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Jordan, I.K. and Bowen, N.J., 2004. Computational analysis of transposable element sequences.
Methods Mol. Biol. 260: 59-71
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Bowen, N.J., Jordan, I.K., Epstein, J.A., Wood, V. and Levin, H.L., 2003. Retrotransposons and their recognition of pol II promoters: A comprehensive survey of the transposable elements derived from the complete genome sequence of Schizosaccharomyces pombe.
Genome Res. 13: 1984-1997
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Jordan, I.K. and Koonin, E.V., 2003. Comparative genomics. Encyclopedia of the Human Genome 1: 897-903 (Cooper, D.N. and M. Calais eds.), Nature Publishing, London, UK
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Jordan, I.K., Henze, K., Fedorova, N.D., Koonin, E.V. and Galperin, M.Y., 2003. Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes.
J. Mol. Microbiol. Biotechnol. 5: 172-189
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Jordan, I.K., Rogozin I.B., Glazko G.V. and Koonin, E.V., 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements.
Trends Genet. 19: 68-72
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Jordan, I.K., Wolf, Y.I. and Koonin, E.V., 2003. No simple dependence between protein evolutionary rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly.
BMC Evolutionary Biology 3: 1
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Jiang, N., Jordan, I.K. and Wessler, S.R., 2002. Dasheng and RIRE2: a non-autonomous LTR element and its putative autonomous partner in the rice genome.
Plant Physiol. 130: 1697-1705
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Bowen, N.J. and Jordan, I.K., 2002. Transposable elements and the evolution of eukaryotic complexity.
Curr. Issues Mol. Biol. 4: 65-76
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Jordan, I.K. and McDonald, J.F., 2002. A biologically active family of human endogeneous retroviruses (HERVs) evolved from an ancient inactive lineage.
Genome Lett. 1: 105-109
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Jordan, I.K., Rogozin, I.B., Wolf, Y.I. and Koonin, E.V., 2002. Microevolutionary genomics of bacteria.
Theor. Popul. Biol. 61: 435-447
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Jordan, I.K., Rogozin, I.B., Wolf, Y.I. and Koonin, E.V., 2002. Essential genes are more evolutionarily conserved than non-essential genes in bacteria.
Genome Res. 12: 962-968
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Rogozin, I.B., Spiridonov, A.N., Sorokin, A.V., Wolf, Y.I., Jordan, I.K., Tatusov, R.L. and Koonin, E.V., 2002. Purifying and directional selection in overlapping prokaryotic genes.
Trends Genet. 18: 228-232
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Jordan, I.K., Kondrashov, F.A., Rogozin, I.B., Tatusov, R.L., Wolf, Y.I. and Koonin, E.V., 2001. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
Genome Biology 2: 0053.1-0053.9
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Jordan, I.K., Natale, D.A., Koonin, E.V. and Galperin, M.Y., 2001. Independent evolution of heavy metal-associated domains in copper chaperones and copper-transporting atpases.
J. Mol. Evol. 53:622-633
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Jordan, I.K., Bishop, G.R. and Gonzalez, D.S., 2001. Sequence and structural aspects of functional diversification in class I alpha-mannosidase evolution.
Bioinformatics 17: 965-976
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Jordan, I.K., Makarova, K.S., Spouge, J.L., Wolf, Y.I. and Koonin, E.V., 2001. Lineage-specific gene expansions in bacterial and archaeal genomes.
Genome Res. 11: 555-565
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Jordan, I.K., Makarova, K.S., Wolf, Y.I. and Koonin, E.V., 2001. Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae.
Trends Genet. 17: 7-10
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Jordan, I.K., Natale, D.A. and Galperin, M.Y., 2000. Copper chaperones in bacteria: association with copper-transporting ATPases.
Trends Biochem. Sci. 25: 480-481
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Gonzalez, D.S. and Jordan, I.K., 2000. The alpha-mannosidases: phylogeny and adaptive diversification.
Mol. Biol. Evol. 17: 292-300
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Jordan, I.K., Sutter, B.A. and McClure, M.A., 2000. Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple protein encoding P gene.
Mol. Biol. Evol. 17: 75-86
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Jordan, I.K. and McDonald, J.F., 1999. Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements.
Genetica 107: 3-13
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Promislow, D.E.L., Jordan, I.K. and McDonald, J.F., 1999. Genomic demography: A life history analysis of transposable element evolution.
Proc. Roy. Soc. Lon. B Biol. 266: 1555-1560
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Jordan, I.K. and McDonald, J.F., 1999. Evidence for the recent horizontal transfer of a long terminal repeat retrotransposon.
Proc. Natl. Acad. Sci. USA 96: 12621-12625
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Jordan, I.K. and McDonald, J.F., 1999. The role of interelement selection in Saccharomyces cerevisiae Ty element evolution.
J. Mol. Evol. 49: 352-357
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Jordan, I.K. and McDonald, J.F., 1999. Tempo and mode of Ty element evolution in Saccharomyces cerevisiae.
Genetics 151: 1341-1351
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Jordan, I.K. and McDonald, J.F., 1999. Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome.
Mol. Biol. Evol. 16: 419-422
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Jordan, I.K. and McDonald, J.F., 1998. Inter-element selection in the regulatory region of the copia retrotransposon.
J. Mol. Evol. 47: 670-676
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Jordan , I.K. and McDonald, J.F., 1998. Evolution of the copia retrotransposon in the Drosophila melanogaster species subgroup.
Mol. Biol. Evol. 15: 1160-1171
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Jordan, I.K. and McDonald, J.F., 1998. Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements.
J. Mol. Evol. 47: 14-20
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McDonald, J.F., Matyunina, L.V., Wilson, S., Jordan, I.K., Bowen, N.J. and Miller, W.J., 1997. LTR retrotransposons and the evolution of eukaryotic enhancers.
Genetica 100: 3-13
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Matyunina, LV., Jordan, I.K. and McDonald, J.F., 1996. Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation.
Proc. Natl. Acad. Sci. USA 93: 7097-7102
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